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A Deep Dive into a Zotero Workflow

I’ve previously posted about Zotero “tips and tricks,” I have a brief review of the beta version of Zotero’s PDF system, and I have an overview of my workflow in Linux, but here I want to do a deep dive into how I conduct note-taking in Zotero. I imagine this can be part of a series where I talk about how Zotero notes flow into Zettlr and from there into drafting out ideas in Libreoffice Writer.

Here, I will offer a two-for-one post: I’ll use my annotations of Derek Caelin’s excellent book chapter on fediverse moderation as examples.


I think the most consistent thing I’ve done over my nearly 15 years (oof I’m old) of using Zotero is taking advantage of the highlighting color palette. Originally, this was limited to Zotero’s notes, but now is part of the PDF annotation.

Currently, Zotero offers a 5-color palette (yellow, red, green, blue, and purple). As I read a PDF in Zotero’s reader, I highlight passages according to this scheme:

  • Yellow are good quotes or things to pay attention to.
  • Red is similar, except “hotter,” so to speak. If yellow means “this is important,” red means “this is really important.”
  • Green are definitions. When authors define their terms, it gets greened.
  • Purple are meta comments from the author about the paper. Things like, “In this article, I argue that…” and “Using a methdology of…”
a screenshot of a note being taken in Zotero
Excellent point! That's a quotable quote.

Anything I highlight in the Zotero PDF reader can be easily added to a corresponding note. These can also be sorted/highlighted in the Zotero PDF annotator, so it’s easy to spot Green (definitions) or Red (“hot” quotes).

What about Blue?

You might notice Blue is missing. This is because I reserve that color for notes to myself. Whenever I take notes on someone’s work, I might put in a comment to myself, such as a connection to another article or an idea I have about how things fit together. Because of this, I don’t really use blue in the PDF, but I do use it in my own notes.

a screenshot of a note being taken in Zotero
This is a blue note. No, not the cool jazz, but a connection I am drawing.

What I do put in the PDF reader is comments on the highlighted portions. These eventually become Blue highlighted sections of the corresponding note. I also put these comments in brackets and italicize them, so it’s very clear these are my own musings.


As I mention in the Tips and Tricks post, I make extensive use of tagging. Zotero’s new PDF annotation system extends tagging into the PDF itself. Each of the highlighted portions can be tagged, and those tags are now searchable in the main Zotero window. This is awesome!

In addition, tags can also be selected in the PDF annotator. Also, quite awesome!

a screenshot of a tag being selected in Zotero's PDF reader
Selecting a tag means the corresponding annotation is selected.

To Synthesis and Beyond

You might notice that all this work is based on a one-to-one, note-to-PDF system. And of course, writing is about synthesizing ideas from across many sources. A weakness of my system is synthesis – blue notes to self won’t cut it. However, I will address that step in another post – and it will focus on Zettlr.

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